.gitmodules

@@ -16,9 +16,6 @@
 [submodule "vendor/rampler"]
 	path = vendor/rampler
 	url = https://github.com/rvaser/rampler
-[submodule "vendor/logger"]
-	path = vendor/logger
-	url = https://github.com/rvaser/logger
 [submodule "vendor/ClaraGenomicsAnalysis"]
 	path = vendor/ClaraGenomicsAnalysis
 	url = https://github.com/clara-genomics/ClaraGenomicsAnalysis

CMakeLists.txt

 cmake_minimum_required(VERSION 3.2)
 project(racon)
-set(racon_version 1.4.7)
+set(racon_version 1.4.10)
 
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
@@ -30,6 +30,7 @@ include_directories(${PROJECT_SOURCE_DIR}/src)
 
 set(racon_sources
     src/main.cpp
+    src/logger.cpp
     src/polisher.cpp
     src/overlap.cpp
     src/sequence.cpp
@@ -58,9 +59,6 @@ endif()
 if (NOT TARGET edlib)
     add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL)
 endif()
-if (NOT TARGET logger)
-    add_subdirectory(vendor/logger EXCLUDE_FROM_ALL)
-endif()
 if (racon_enable_cuda)
     if (DEFINED CLARAGENOMICSANALYSIS_SDK_PATH)
         list(APPEND CMAKE_PREFIX_PATH "${CLARAGENOMICSANALYSIS_SDK_PATH}/cmake")
@@ -90,7 +88,7 @@ if (racon_enable_cuda)
     endif()
 endif()
 
-target_link_libraries(racon bioparser spoa thread_pool edlib_static logger)
+target_link_libraries(racon bioparser spoa thread_pool edlib_static)
 if (racon_enable_cuda)
     target_link_libraries(racon cudapoa cudaaligner)
 endif()
@@ -106,6 +104,7 @@ if (racon_build_tests)
 
     set(racon_test_sources
         test/racon_test.cpp
+        src/logger.cpp
         src/polisher.cpp
         src/overlap.cpp
         src/sequence.cpp
@@ -123,7 +122,7 @@ if (racon_build_tests)
         add_subdirectory(vendor/googletest/googletest EXCLUDE_FROM_ALL)
     endif()
 
-    target_link_libraries(racon_test bioparser spoa thread_pool edlib_static logger gtest_main)
+    target_link_libraries(racon_test bioparser spoa thread_pool edlib_static gtest_main)
     if (racon_enable_cuda)
         target_link_libraries(racon_test cudapoa cudaaligner)
     endif()

debian/changelog

-racon (1.4.7-1) UNRELEASED; urgency=medium
+racon (1.4.10-1) unstable; urgency=medium
 
+  * Team upload.
+
+  [ Andreas Tille ]
   * New upstream version
   * debhelper-compat 12
   * Standards-Version: 4.4.0
-  * Build-Depends: liblogger-dev
-    Closes: #940564
   * Point watch file to new location
   * New homepage
   * Versioned Build-Depends: libthread-pool-dev (>= 2)
-  * New upstream version
-  * New upstream version
 
- -- Andreas Tille <tille@debian.org>  Wed, 18 Sep 2019 11:43:24 +0200
+  [ Michael Crusoe ]
+  * New upstream version Closes: #940564
+  * Run the tests during the build
+  * Run the tests as part of 'autopkgtest'ing
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 12 Nov 2019 14:43:58 +0100
 
 racon (1.3.2-1) unstable; urgency=medium
 

debian/control

@@ -11,7 +11,6 @@ Build-Depends: debhelper-compat (= 12),
                libedlib-dev,
                libspoa-dev,
                libthread-pool-dev (>= 2),
-               liblogger-dev,
                rampler
 Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/racon
@@ -22,6 +21,7 @@ Package: racon
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Recommends: python3
 Description: consensus module for raw de novo DNA assembly of long uncorrected reads
  Racon is intended as a standalone consensus module to correct raw
  contigs generated by rapid assembly methods which do not include a

debian/examples

+test/data

debian/install

+obj-*/bin/racon_test /usr/lib/racon/
+scripts/racon_wrapper.py /usr/bin/

debian/patches/py3

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Mark script as being Python version 3
+--- racon.orig/scripts/racon_wrapper.py
++++ racon/scripts/racon_wrapper.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ from __future__ import print_function
+ import os, sys, time, shutil, argparse, subprocess

debian/patches/remove_buildpath

+From: Michael R. Crusoe <michael.crusoe>
+Subject: remove unnecessary __FILE__ reference
+
+It reduces the reproduciblilty of the build
+--- racon.orig/src/polisher.cpp
++++ racon/src/polisher.cpp
+@@ -143,8 +143,7 @@
+ #else
+         fprintf(stderr, "[racon::createPolisher] error: "
+                 "Attemping to use CUDA when CUDA support is not available.\n"
+-                "Please check logic in %s:%s\n",
+-                __FILE__, __func__);
++                "Please check logic in scripts/racon_wrapper.py:%s\n", __func__);
+         exit(1);
+ #endif
+     }
+--- racon.orig/test/racon_test_config.h.in
++++ racon/test/racon_test_config.h.in
+@@ -6,4 +6,4 @@
+ 
+ #include <string>
+ 
+-const std::string racon_test_data_path = "@racon_test_data_path@";
++const std::string racon_test_data_path = "./data/";

debian/patches/series

 use_debian_packaged_libs.patch
+remove_buildpath
+py3

debian/patches/use_debian_packaged_libs.patch

@@ -2,9 +2,9 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update:  Fri, 08 Jun 2018 13:20:51 +0200
 Description: Use Debian packaged libraries
 
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -46,21 +46,6 @@ endif()
+--- racon.orig/CMakeLists.txt
++++ racon/CMakeLists.txt
+@@ -47,18 +47,6 @@
  # Add version information to bibary.
  target_compile_definitions(racon PRIVATE RACON_VERSION="v${racon_version}")
  
@@ -19,25 +19,21 @@ Description: Use Debian packaged libraries
 -endif()
 -if (NOT TARGET edlib)
 -    add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL)
--endif()
--if (NOT TARGET logger)
--    add_subdirectory(vendor/logger EXCLUDE_FROM_ALL)
 -endif()
  if (racon_enable_cuda)
      if (DEFINED CLARAGENOMICSANALYSIS_SDK_PATH)
          list(APPEND CMAKE_PREFIX_PATH "${CLARAGENOMICSANALYSIS_SDK_PATH}/cmake")
-@@ -90,7 +75,9 @@ if (racon_enable_cuda)
+@@ -88,7 +76,8 @@
      endif()
  endif()
  
--target_link_libraries(racon bioparser spoa thread_pool edlib_static logger)
-+#set_target_properties(racon PROPERTIES COMPILE_FLAGS -pthread LINK_FLAGS -pthread) # does not work
-+target_link_libraries(racon spoa thread_pool edlib logger z)
+-target_link_libraries(racon bioparser spoa thread_pool edlib_static)
++target_link_libraries(racon spoa thread_pool edlib z)
 +set_target_properties(racon PROPERTIES COMPILE_FLAGS -pthread LINK_FLAGS -pthread)
  if (racon_enable_cuda)
      target_link_libraries(racon cudapoa cudaaligner)
  endif()
-@@ -119,11 +106,7 @@ if (racon_build_tests)
+@@ -118,11 +107,7 @@
          add_executable(racon_test ${racon_test_sources})
      endif()
  
@@ -45,8 +41,8 @@ Description: Use Debian packaged libraries
 -        add_subdirectory(vendor/googletest/googletest EXCLUDE_FROM_ALL)
 -    endif()
 -
--    target_link_libraries(racon_test bioparser spoa thread_pool edlib_static logger gtest_main)
-+    target_link_libraries(racon_test spoa thread_pool pthread edlib logger gtest_main gtest z)
+-    target_link_libraries(racon_test bioparser spoa thread_pool edlib_static gtest_main)
++    target_link_libraries(racon_test spoa thread_pool pthread edlib gtest_main gtest z)
      if (racon_enable_cuda)
          target_link_libraries(racon_test cudapoa cudaaligner)
      endif()

debian/rules

@@ -12,3 +12,8 @@ override_dh_auto_configure:
 	# Somehow the means in the patch for CMakeLists.txt to replace -lpthread by -pthread to not work
 	# Just hack it here
 	sed -i 's/-lpthread/-pthread/' obj-*/CMakeFiles/racon_test.dir/link.txt
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	cd test && ../obj-*/bin/racon_test
+endif

debian/tests/control

+Test-Command: sh -c "cd /usr/share/doc/racon/examples && /usr/lib/racon/racon_test"
+Depends: @
+Restrictions: allow-stderr

src/cuda/cudapolisher.cpp

@@ -10,11 +10,11 @@
 #include <cuda_profiler_api.h>
 
 #include "sequence.hpp"
+#include "logger.hpp"
 #include "cudapolisher.hpp"
 #include <claragenomics/utils/cudautils.hpp>
 
 #include "bioparser/bioparser.hpp"
-#include "logger/logger.hpp"
 
 namespace racon {
 

src/logger.cpp

+/*!
+ * @file logger.cpp
+ *
+ * @brief Logger source file
+ */
+
+#include <iostream>
+
+#include "logger.hpp"
+
+namespace racon {
+
+Logger::Logger()
+        : time_(0.), bar_(0), time_point_() {
+}
+
+Logger::~Logger() {
+}
+
+void Logger::log() {
+    auto now = std::chrono::steady_clock::now();
+    if (time_point_ != std::chrono::time_point<std::chrono::steady_clock>()) {
+        time_ += std::chrono::duration_cast<std::chrono::duration<double>>(now - time_point_).count();
+    }
+    time_point_ = now;
+}
+
+void Logger::log(const std::string& msg) const {
+    std::cerr << msg << " " << std::fixed
+        << std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
+        << " s" << std::endl;
+}
+
+void Logger::bar(const std::string& msg) {
+    ++bar_;
+    std::string progress_bar = "[" + std::string(bar_, '=') + (bar_ == 20 ? "" : ">" + std::string(19 - bar_, ' ')) + "]";
+
+    std::cerr << msg << " " << progress_bar << " " << std::fixed
+        << std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
+        << " s";
+
+    bar_ %= 20;
+    if (bar_ == 0) {
+        std::cerr << std::endl;
+    } else {
+        std::cerr << "\r";
+    }
+}
+
+void Logger::total(const std::string& msg) const {
+    std::cerr << msg << " " << std::fixed
+        << time_ + std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
+        << " s" << std::endl;
+}
+
+}

src/logger.hpp

+/*!
+ * @file logger.hpp
+ *
+ * @brief Logger header file
+ */
+
+#pragma once
+
+#include <cstdint>
+#include <chrono>
+#include <string>
+
+namespace racon {
+
+static const std::string version = "v1.0.0";
+
+class Logger {
+public:
+    Logger();
+
+    Logger(const Logger&) = default;
+    Logger& operator=(const Logger&) = default;
+
+    Logger(Logger&&) = default;
+    Logger& operator=(Logger&&) = default;
+
+    ~Logger();
+
+    /*!
+     * @brief Resets the time point
+     */
+    void log();
+
+    /*!
+     * @brief Prints the elapsed time from last time point to stderr
+     */
+    void log(const std::string& msg) const;
+
+    /*!
+     * @brief Prints a progress bar and the elapsed time from last time to
+     * stderr (the progress bar resets after 20 calls)
+     */
+    void bar(const std::string& msg);
+
+    /*!
+     * @brief Prints the total elapsed time from the first log() call
+     */
+    void total(const std::string& msg) const;
+
+private:
+    double time_;
+    std::uint32_t bar_;
+    std::chrono::time_point<std::chrono::steady_clock> time_point_;
+};
+
+}

src/polisher.cpp

@@ -11,6 +11,7 @@
 #include "overlap.hpp"
 #include "sequence.hpp"
 #include "window.hpp"
+#include "logger.hpp"
 #include "polisher.hpp"
 #ifdef CUDA_ENABLED
 #include "cuda/cudapolisher.hpp"
@@ -19,7 +20,6 @@
 #include "bioparser/bioparser.hpp"
 #include "thread_pool/thread_pool.hpp"
 #include "spoa/spoa.hpp"
-#include "logger/logger.hpp"
 
 namespace racon {
 
@@ -170,7 +170,7 @@ Polisher::Polisher(std::unique_ptr<bioparser::Parser<Sequence>> sparser,
         alignment_engines_(), sequences_(), dummy_quality_(window_length, '!'),
         window_length_(window_length), windows_(),
         thread_pool_(thread_pool::createThreadPool(num_threads)),
-        thread_to_id_(), logger_(new logger::Logger()) {
+        thread_to_id_(), logger_(new Logger()) {
 
     uint32_t id = 0;
     for (const auto& it: thread_pool_->thread_identifiers()) {

src/polisher.hpp

@@ -25,15 +25,13 @@ namespace spoa {
     class AlignmentEngine;
 }
 
-namespace logger {
-    class Logger;
-}
 
 namespace racon {
 
 class Sequence;
 class Overlap;
 class Window;
+class Logger;
 
 enum class PolisherType {
     kC, // Contig polishing
@@ -95,7 +93,7 @@ protected:
     std::unique_ptr<thread_pool::ThreadPool> thread_pool_;
     std::unordered_map<std::thread::id, uint32_t> thread_to_id_;
 
-    std::unique_ptr<logger::Logger> logger_;
+    std::unique_ptr<Logger> logger_;
 };
 
 }

src/window.cpp

@@ -42,6 +42,10 @@ Window::~Window() {
 void Window::add_layer(const char* sequence, uint32_t sequence_length,
     const char* quality, uint32_t quality_length, uint32_t begin, uint32_t end) {
 
+    if (sequence_length == 0 || begin == end) {
+        return;
+    }
+
     if (quality != nullptr && sequence_length != quality_length) {
         fprintf(stderr, "[racon::Window::add_layer] error: "
             "unequal quality size!\n");